Periodic Release Version

I have been inconsistent with creating specific releases and updating package versions in this codebase.

This is a substantial update in functionality and performance relative to the previous released version, with massive changes to the workflow(s) and input file formats to operate.

In general I don't recommend you strictly stick to 'official' releases, but I will attempt to differentiate better between ongoing developmental versions and substantial operational updates.

Remove separate history files

What's Changed

Several substantial changes, the main ones which come to mind:

• Talos now uses a Pedigree, optionally in an extended format with an extra column to contain HPO terms, instead of taking a pedigree and phenopackets file
• The de novo event detection process now includes some flexibility for observed data formats which previously caused breakages
• Instead of tracking results and 'history' separately, Talos now takes previous results as input to maintain state.

This release also includes two new optional files, used to map the VCF/MT sample IDs to an external ID, or a Seqr ID. These have been added to the Talos NextFlow config file with dummy values here. If you previously generated a run-specific config file for your data, and are moving up to this release, you will need to add these entries to your config to prevent run failures.

Full Changelog: 7.1.5...8.0.2

7.1.5

What's Changed

Multiple changes, a few flip-flops on how Nextflow outputs are extracted from the working directory. I've settled on a COPY for all outputs, which is handled well by Nextflow assuming a local-like file structure. This may not work on cloud/some HPC deployments, but works in a handful of HPC tests and as a local test run.

The PanelApp phase now generates a PanelApp dump using highly parallelised queries, and then loads/parses that data dump instead of interacting with PanelApp with each run. This is a net simplification of the overall workflow, and enables the deployment of Talos in situations where the worker nodes/env won't have open internet access.

• (feat)522: insert AC/AF/AN by @MattWellie in #523
• Fix: Add --no-same-owner flag to tar extraction commands to resolve Docker-to-macOS permission issues by @lgruen in #514
• Pre download panelapp, adjust Talos to accommodate by @MattWellie in #524
• Mention AlphaMissense in the large_files requirements by @lgruen in #513
• Fix talos stages.py by @MattWellie in #526
• Dont retain panels without green genes by @MattWellie in #527
• Update config as cohort input MTs aren't tar'd up anymore by @lgruen-vcgs in #530
• Fix: correction to gff3 processing, and better nextflow output management by @MattWellie in #531
• RD-122: Persistent urls by @MattWellie in #532
• Update NF module to COPY MT out by @MattWellie in #534
• Correction to metamist query parameter by @MattWellie in #536

Full Changelog: 7.0.11...7.1.5

Remove PL values from consideration

What's Changed

• Correction to manually overriding clinvarbitration results by @MattWellie in #519
• Documentation bump by @MattWellie in #521

PL is no longer a required annotation in VCF/MTs. The de novo test where it was used is now solely based on the AD/GQ/GT fields in each trio. This feels fine, as PL and GQ are derived from the same information, so there was some redundancy there anyway.

Full Changelog: 7.0.9...7.0.11

Insert derived PL values

What's Changed

• Re-add PL substitution derived from GQ by @MattWellie in #518

If the input VCF/MT doesn't have PL scores, these will be generated and inserted based on the GQ scores (which are mandatory). This reinstates some pre-existing functionality, which was part of the de novo calculation method. These artificial PL scores only exist within the context of the PL scores, and are not retained for general use.

Full Changelog: 7.0.8...7.0.9

7.0.8

What's Changed

• Workflow patch for vc by @MattWellie in #512

Full Changelog: 7.0.7...7.0.8

7.0.7 - Patch to latest NextFlow modules

What's Changed

• Flexible hpo terms missing by @MattWellie in #506
• Allow usage of externally generated callset by @MattWellie in #508
• Update NextFlow for single VCF/normalisation by @MattWellie in #509

Full Changelog: 7.0.4...7.0.7

Updated Filtering, Improved Deployment Experience

What's Changed

• Remove seqr link text by @MattWellie in #501
• Migrate to cpg-flow by @MattWellie in #502
• Alter how filters are configured and applied by @MattWellie in #503
• Make Nextflow more easily deployable by @MattWellie in #505

Full Changelog: v7.0.2...7.0.4

v7.0.2

What's Changed

• Landing content update by @MattWellie in #497
• Patch nf modules by @MattWellie in #498
• Fix CNV parsing by @MattWellie in #499

Full Changelog: v7.0.1...v7.0.2

Patch to SVannotate VCF parsing

What's Changed

• Add custom Gene-MOI data by @MattWellie in #494
• SV parsing patch by @MattWellie in #495

Full Changelog: v7.0.0...v7.0.1